MicroLecE2Ch8 Flashcards
Genetics
Study of what genes, how they carry info, how info is expressed, how genes replicate
Gene
Segment of DNA that encodes a functional product, usually a protein
Not all DNA codes for a functional product, only the ones who do are considered genes
Chromosome
Structure containing all DNA (junk DNA + genes) that physically carries hereditary info
Contain the genes
Genome
All the genetic info in a cell
Genomics
Molecular study of genomes
Genotype
Genes of an organism, what the gene is
Ex: genotype codes for blue eyes
Phenotype
Expression of the genes – physical representation
Ex: phenotype is blue eyes
Determining Relatedness
Takes the genetic code of one species and line it up with other species
Compares nucleotide sequence, the more similar in sequence the more related
Determine what percent is identical btwn species
Genetic Maps
Cartoon illustration of circle that resembles a bacteria chromosome where all the known genes can be plotted on
Central Dogma/Flow of Genetic Information
DNA –> RNA –> Protein
Expression: genetic info is used w/in a cell to produce the proteins. Going from DNA to protein
Recombination: genetic info can be exchanged btwn cells of the same generation so it can evolve. Only way bacteria can exchange genetic info b/c it doesn’t do sexual replication
Replication: genetic info can be transferred btwn generations of cells – parent cell to two daughter cells
DNA Structure
Made up of 4 primary nucleotides – A, T, C, G
Double helix associated w/proteins
Backbone is deoxyribose-phosphate (sugar ring)
Strands held together by hydrogen bonds btwn A-T and C-G
Antiparallel: the sugar-phosphate backbone of one strand is upside down relative to the backbone of the other strand
All chemical rxns happen off the 3’ end with the OH (hydroxyl group), a nucleotide cannot connect/add onto the 5’ end with the phosphate group
Semiconservative Replication
Conservative b/c each daughter cell will have 1 original DNA strand from the parent cell (conservative) but only SEMI-conservative b/c the other strand which is the new strand will just be a copy of the original strand
DNA Replication - General
Binary Fission
Takes the double helix and pulls it apart and makes a copy by adding in the appropriate nucleotides to each of the daughter strands. End up producing two identical strands
DNA Polymerase
Enzyme that catalyzes the hydrolysis rxn that adds on a nucleotide each time
Takes DNA and makes a DNA copy
DNA Replication - Process
1) Replication Bubble, Replication forks
2) Replication begins at the Ori (origin)
3) Top strand runs from 5’ to 3’, Bottom strand runs from 5’ to 3’
4) DNA Polymerase starts laying a new nucleotide over and over as the bubble keeps on the top strand – Leading Strand
5) On the bottom strand – Lagging Strand, an RNA Primer (there are multiple RNA Primers) is laid close to the bubble that has a 3’ OH hanging off it that DNA Polymerase needs to add a nucleotide. DNA Polymerase will add nucleotides behind each RNA Primer. RNA Primer + DNA that has been filled in behind it = Okazaki Fragment. Once there is a complete Okazaki Fragment, DNA Polymerase (DNA Ligase) will remove the RNA Primer and use the 3’ OH that is available due to the DNA that has already been put in, and fill that back in resulting in a complete strand of DNA
DNA Replication - Summary
1) Replication Bubble, Replication forks
2) Replication begins at the Ori (origin)
3) Leading Strand: Top 1/2 of strand goes 5’ to 3’, there is a 3’ OH so DNA Polymerase can just follow the bubble and keep adding in nucleotides as the bubble continues to open
4) Lagging Strand: On bottom 1/2 of strand, there is no 3’ OH hanging off so an RNA Primer is laid, DNA Polymerase extends that to the next RNA Primer. The RNA Primer + DNA that is laid is called the Okazaki Fragment. Once that is done, the RNA Primer is pulled out and is replaced with DNA
Transcription - General
DNA –> RNA (making an RNA transcript of the DNA)
Goal: to make RNA
RNA Polymerase makes RNA
3 Different Types of RNA that can be made: mRNA (ends up becoming protein, messenger RNA), tRNA (specialized little pieces of RNA involved in translation, bring amino acids for translation, transport RNA), Ribosomal RNA (makes up ribosomes, involved in translation
Transcription - Process
1) Every gene starts at a Promoter – a specific sequence on the DNA that signals when the gene starts, and ends at a Terminator - specific sequence that tells RNA Polymerase where the gene stops
2) Occurs 5’ to 3’
3) 2 strands are pulled apart
4) Starts at the Promoter, RNA Polymerase binds and moves along in the 5’ to 3’ direction and match each nucleotide to the corresponding nucleotide, but b/c making RNA matches A to Uracil. RNA is single stranded
5) RNA Polymerase ill continue until it reaches the Terminator sequence and then it will disassociate leaving mRNA
In Prokaryotes, mRNA can go directly into translation
In Eukaryotes, there are introns (junk DNA) so before mRNA can enter translation, the introns must be cut out
Translation - General
RNA –> Protein
Translation - Process
1) DNA sequence – 4 nucleotides A, U, G, C
2) 70S Ribosome reads in sets of 3 known as codons and adds the amino acid a codon codes for
3) Starts at the start codon (AUG)
4) Each codon codes for a specific amino acid
5) Ribosome knows when to stop adding amino acids to make proteins when it reaches a stop codons/nonsense codon
64 different codons, multiple codons can read for the same amino acid
Why is genetic code considered “degenerate”?
B/c the first two letters in the codon are identical but the last is different. important b/c if the cell messes up and puts in the wrong letter in the 3rd position, it will still make the same amino acid – way for the cell to self-regulate against mutation
If amino acid is wrong, can change the whole functionality of the protein
Translation - Summary
1) mRNA comes off in transcription, ribosome starts scanning it looking for the start codon
2) Once start codon is located, ribosome clamps down on it, tRNA will bring in a complementary anticodon that will pair w/the codon on the mRNA, resulting in an amino acid
3) Ribosome keeps moving down the mRNA, reading in sets of 3, each set of 3 a new tRNA (are recycled) comes in, matches its anticodon to the codon and adds on the new amino acid
4) Keeps going until Ribosome reads a stop codon/nonsense codon, ribosome disassociates, mRNA is done, leaves a new protein that can fold into a secondary and tertiary structures
Genetic Expression
Transcription and Translation
Constitutive Gene
Always on, expressed at a fixed rate
Repressible Gene
Default in on, if not needed it can be turned off
Genes involved in anabolic rxns
Exs: tryptophan, glycine
Inducible Gene
Default is off, if needed can be turned on
Genes involved in catabolic rxns
Ex: genes involved in breaking down mannose
Operon
Overall components that make up a gene
Promoter, Operator, structural genes
RNA Polymerase binds to Promoter and Operator
Induction
Default being blocked by a repressor unless the inducer that removes the repressor is present and then RNA Polymerase can then make copies of the gene
Repression
Default is on, no repressor. But if there is too much of the repressible gene, the gene will bind to repressor protein, the shape will change and RNA polymerase can no longer make more of the repressible gene
Mutation
Change in the genetic material
Can be beneficial, harmful, or neutral
How do mutations occur?
2 ways:
1) Exposure to a mutagen (outside force)
2) Spontaneous mutation
Mutagen
Outside force that causes a mutation
Point Mutation
One nucleotide gets changed
Different types of point mutations
Missense mutation
One nucleotide is changed
Point mutation that alters the function of the protein but does not destroy it
Nonsense mutation
Inserts a stop codon in the middle of the protein
Point mutation that alters the function of the protein and destroys it
Frameshift mutation
NOT a point mutation
One nucleotide pair is inserted or removed. Destroys the protein
Spontaneous mutation
Occur from DNA and RNA Polymerase causes it by accident
Rarely happens
Chemical Mutagens
Chemical mutagen is defined as causing a mutation every 1,000 base pairs
Analogs that look similar enough to a nucleotide that it fools DNA Polymerase or RNA Polymerase into using it
Ionizing Radiation
Has a short wavelength, packs a lot of energy, can cause rearrangment of electrons
UV Radiation
Can cause mutations and skin cancer
When there are two thymines next to each other that are supposed to be hydrogen bonded to adenines. when UV radiation hits it, it breaks the hydrogen bonds and causes the two thymines to double bond to each other. Causes DNA to bubble up. When DNA or RNA Polymerase comes along, it gets stuck at the bubble and cannot go any further. Whatever gene it is encoding for, the body can no longer make.
Repair
Nucleotide Excision Repair: photolyase separates thymine dimers and fill it in with new DNA to repair it
Vertical Gene Transfer
Sexual reproduction – direct exchange of genetic info
Bacteria cannot do this
Horizontal Gene Transfer
Exchanging genetic info btwn parent cells
Only way bacteria can vary their genetic info which is important for evolution
1) Recombination
2) Transformation
3) Transduction
Recombination
Cell shares w/itself
Exchange of genes btwn 2 DNA molecules in a cell
Transformation
Uptake of naked DNA (not associated w/anything)
Conjugation
Cell to Cell DNA transfer
Some cells are F+ cells – have the conjugation plasmid separate from its genome (circular piece of DNA that codes for the pili gene). All other cells are F- and do not have the plasmid. An F+ cell sends its DNA/conjugative plasmid over to the F- cells through its pili. The F- cells turn to F+ cells
Considered a sexual process, not reproduction, b/c there is a direct exchange of genetic info
Important b/c a lot of the genes found on the F+ plasmid are antibiotic resistant and can conjugate w/other bacteria in the body and give them antibiotic resistance too
Different species can conjugate w/each other
Transduction
Transfer of DNA via a virus
A phage (virus) attacks and injects its DNA into the bacteria
The virus will reproduce w/in the bacterial cell
When its done reproducing, it makes adult viruses again that will burst out of the cell
Sometimes when the virus packages up its viral DNA it takes some of the bacterial DNA w/it, so when the virus attacks another bacterial cell it gives that cell not only the viral DNA but the bacterial DNA
So it is allowing genetic exchange btwn two bacteria, b/c bacterial cell now has a new set of bacterial genes that it can choose to include in its chromosome
